Cancer Biomarkers and Big Data: A Planetary Science Approach.

Cancer biomarker research has become a data-intensive discipline requiring innovative approaches for data analysis that can combine traditional and data-driven methods. Significant leveraging can be done transferring methodologies and capabilities across scientific disciplines, such as planetary science and astronomy, each of which are grappling with and developing similar solutions for the analysis of massive scientific data.

Summarizing performance for genome scale measurement of miRNA: reference samples and metrics.

BACKGROUND: The potential utility of microRNA as biomarkers for early detection of cancer and other diseases is being investigated with genome-scale profiling of differentially expressed microRNA. Processes for measurement assurance are critical components of genome-scale measurements. Here, we evaluated the utility of a set of total RNA samples, designed with between-sample differences in the relative abundance of miRNAs, as process controls. RESULTS: Three pure total human RNA samples (brain, liver, and placenta) and two different mixtures of these components were evaluated as measurement assurance control samples on multiple measurement systems at multiple sites and over multiple rounds. In silico modeling of mixtures provided benchmark values for comparison with physical mixtures. Biomarker development laboratories using next-generation sequencing (NGS) or genome-scale hybridization assays participated in the study and returned data from the samples using their routine workflows. Multiplexed and single assay reverse-transcription PCR (RT-PCR) was used to confirm in silico predicted sample differences. Data visualizations and summary metrics for genome-scale miRNA profiling assessment were developed using this dataset, and a range of performance was observed. These metrics have been incorporated into an online data analysis pipeline and provide a convenient dashboard view of results from experiments following the described design. The website also serves as a repository for the accumulation of performance values providing new participants in the project an opportunity to learn what may be achievable with similar measurement processes. CONCLUSIONS: The set of reference samples used in this study provides benchmark values suitable for assessing genome-scale miRNA profiling processes. Incorporation of these metrics into an online resource allows laboratories to periodically evaluate their performance and assess any changes introduced into their measurement process.

Evaluating the Appropriateness of Downscaled Climate Information for Projecting Risks of Salmonella.

Foodborne diseases have large economic and societal impacts worldwide. To evaluate how the risks of foodborne diseases might change in response to climate change, credible and usable climate information tailored to the specific application question is needed. Global Climate Model (GCM) data generally need to, both, be downscaled to the scales of the application to be usable, and represent, well, the key characteristics that inflict health impacts. This study presents an evaluation of temperature-based heat indices for the Washington D.C. area derived from statistically downscaled GCM simulations for 1971-2000--a necessary step in establishing the credibility of these data. The indices approximate high weekly mean temperatures linked previously to occurrences of Salmonella infections. Due to bias-correction, included in the Asynchronous Regional Regression Model (ARRM) and the Bias Correction Constructed Analogs (BCCA) downscaling methods, the observed 30-year means of the heat indices were reproduced reasonably well. In April and May, however, some of the statistically downscaled data misrepresent the increase in the number of hot days towards the summer months. This study demonstrates the dependence of the outcomes to the selection of downscaled climate data and the potential for misinterpretation of future estimates of Salmonella infections.

Big Data Challenges in Climate Science.

The knowledge we gain from research in climate science depends on the generation, dissemination, and analysis of high-quality data. This work comprises technical practice as well as social practice, both of which are distinguished by their massive scale and global reach. As a result, the amount of data involved in climate research is growing at an unprecedented rate. Climate model intercomparison (CMIP) experiments, the integration of observational data and climate reanalysis data with climate model outputs, as seen in the Obs4MIPs, Ana4MIPs, and CREATE-IP activities, and the collaborative work of the Intergovernmental Panel on Climate Change (IPCC) provide examples of the types of activities that increasingly require an improved cyberinfrastructure for dealing with large amounts of critical scientific data. This paper provides an overview of some of climate science's big data problems and the technical solutions being developed to advance data publication, climate analytics as a service, and interoperability within the Earth System Grid Federation (ESGF), the primary cyberinfrastructure currently supporting global climate research activities.